Dear Sir,
Kinetis KL25 has a PIT module with two channels. When you execute the procedure pointed from the PIT vector (i.e. the isr linked to the interrupt you can read the Timer Flag Register (PIT_TFLGn) of the channel 0 and channel 1. The one with the bit field TIF set to one has generated the interrupt request. Reading it the flag will be cleared, as describer in the Reference Manual at chapter 32.3.7.
Best Regards